I just usually have DF open in the background while i work. I've never really done a megaproject on this fort, just many survival oriented buildings and a lot of failed projects. (Walling up the caverns cost me a lot of dwarves.) Once i got the fort running safely and walled off the surface, i could leave it fairly safely for long periods of time. i played much more actively for the first ~75 years while i was trying to get everything working. I edited the announcements file to make it pause when a dwarf died and killed off all the animals, so i never had surprise reanimation after the first couple of times stupid mistakes almost got me. The whole fort is deliberately compartmentalized; a raging dwarf in my first fort killed over 40 dwarves because i couldn't stop him, this way i can just lock him in and he'll starve.
As to the dead unit memory cleaner thingie, that could be really good. There's 9k dead in this fort.
The goblins executed the titan in about 10 seconds, then its reanimated corpse and the local undead wildlife that never leaves killed all the goblins eventually. Side note, undead things seem to keep their building destroyer and trapavoid status. The damn titan corpse cut a miner's arm off and shattered a child's lower spine. That and troll corpses keep breaking doors that are unlocked! They can walk right through, they just seem to prefer to wreck an iron door.